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Yasar Yildiz S, Finore I, Leone L, Romano I, Lama L, Kasavi C, Nicolaus B, Toksoy Oner E, Poli A. Genomic Analysis Provides New Insights Into Biotechnological and Industrial Potential of Parageobacillus thermantarcticus M1. Front Microbiol 2022; 13:923038. [PMID: 35756030 PMCID: PMC9218356 DOI: 10.3389/fmicb.2022.923038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/18/2022] [Indexed: 02/02/2023] Open
Abstract
Parageobacillus thermantarcticus strain M1 is a Gram-positive, motile, facultative anaerobic, spore forming, and thermophilic bacterium, isolated from geothermal soil of the crater of Mount Melbourne (74°22′ S, 164°40′ E) during the Italian Antarctic Expedition occurred in Austral summer 1986–1987. Strain M1 demonstrated great biotechnological and industrial potential owing to its ability to produce exopolysaccharides (EPSs), ethanol and thermostable extracellular enzymes, such as an xylanase and a β-xylosidase, and intracellular ones, such as xylose/glucose isomerase and protease. Furthermore, recent studies revealed its high potential in green chemistry due to its use in residual biomass transformation/valorization and as an appropriate model for microbial astrobiology studies. In the present study, using a systems-based approach, genomic analysis of P. thermantarcticus M1 was carried out to enlighten its functional characteristics. The elucidation of whole-genome organization of this thermophilic cell factory increased our understanding of biological mechanisms and pathways, by providing valuable information on the essential genes related to the biosynthesis of nucleotide sugar precursors, monosaccharide unit assembly, as well as the production of EPSs and ethanol. In addition, gene prediction and genome annotation studies identified genes encoding xylanolytic enzymes that are required for the conversion of lignocellulosic materials to high-value added molecules. Our findings pointed out the significant potential of strain M1 in various biotechnological and industrial applications considering its capacity to produce EPSs, ethanol and thermostable enzymes via the utilization of lignocellulosic waste materials.
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Affiliation(s)
- Songul Yasar Yildiz
- Department of Bioengineering, Istanbul Medeniyet University, Istanbul, Turkey
| | - Ilaria Finore
- Institute of Biomolecular Chemistry (ICB), National Research Council, Naples, Italy
| | - Luigi Leone
- Institute of Biomolecular Chemistry (ICB), National Research Council, Naples, Italy
| | - Ida Romano
- Institute of Biomolecular Chemistry (ICB), National Research Council, Naples, Italy
| | - Licia Lama
- Institute of Biomolecular Chemistry (ICB), National Research Council, Naples, Italy
| | - Ceyda Kasavi
- Department of Bioengineering, Industrial Biotechnology and Systems Biology (IBSB), Marmara University, Istanbul, Turkey
| | - Barbara Nicolaus
- Institute of Biomolecular Chemistry (ICB), National Research Council, Naples, Italy
| | - Ebru Toksoy Oner
- Department of Bioengineering, Industrial Biotechnology and Systems Biology (IBSB), Marmara University, Istanbul, Turkey
| | - Annarita Poli
- Institute of Biomolecular Chemistry (ICB), National Research Council, Naples, Italy
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Romano I, Camerlingo C, Vaccari L, Birarda G, Poli A, Fujimori A, Lepore M, Moeller R, Di Donato P. Effects of Ionizing Radiation and Long-Term Storage on Hydrated vs. Dried Cell Samples of Extremophilic Microorganisms. Microorganisms 2022; 10:190. [PMID: 35056640 PMCID: PMC8782055 DOI: 10.3390/microorganisms10010190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 01/04/2023] Open
Abstract
A main factor hampering life in space is represented by high atomic number nuclei and energy (HZE) ions that constitute about 1% of the galactic cosmic rays. In the frame of the "STARLIFE" project, we accessed the Heavy Ion Medical Accelerator (HIMAC) facility of the National Institute of Radiological Sciences (NIRS) in Chiba, Japan. By means of this facility, the extremophilic species Haloterrigena hispanica and Parageobacillus thermantarcticus were irradiated with high LET ions (i.e., Fe, Ar, and He ions) at doses corresponding to long permanence in the space environment. The survivability of HZE-treated cells depended upon either the storage time and the hydration state during irradiation; indeed, dry samples were shown to be more resistant than hydrated ones. With particular regard to spores of the species P. thermantarcticus, they were the most resistant to irradiation in a water medium: an analysis of the changes in their biochemical fingerprinting during irradiation showed that, below the survivability threshold, the spores undergo to a germination-like process, while for higher doses, inactivation takes place as a consequence of the concomitant release of the core's content and a loss of integrity of the main cellular components. Overall, the results reported here suggest that the selected extremophilic microorganisms could serve as biological model for space simulation and/or real space condition exposure, since they showed good resistance to ionizing radiation exposure and were able to resume cellular growth after long-term storage.
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Affiliation(s)
- Ida Romano
- Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei, 34, 80078 Pozzuoli, Italy; (I.R.); (A.P.)
| | - Carlo Camerlingo
- SuPerconducting and Other INnovative Materials and Devices Institute, National Research Council of Italy, Via Campi Flegrei, 34, 80078 Pozzuoli, Italy;
| | - Lisa Vaccari
- Elettra—Sincrotrone Trieste S.C.p.A. S.S., 14 km 163,5 in Area Science Park, Basovizza, 34149 Trieste, Italy; (L.V.); (G.B.)
| | - Giovanni Birarda
- Elettra—Sincrotrone Trieste S.C.p.A. S.S., 14 km 163,5 in Area Science Park, Basovizza, 34149 Trieste, Italy; (L.V.); (G.B.)
| | - Annarita Poli
- Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei, 34, 80078 Pozzuoli, Italy; (I.R.); (A.P.)
| | - Akira Fujimori
- Molecular and Cellular Radiation Biology Group, Department of Charged Particle Therapy Research, Institute for Quantum Medical Science, Chiba 263-8555, Japan;
| | - Maria Lepore
- Dipartimento di Medicina Sperimentale, Università della Campania “L. Vanvitelli”, Via S. Maria di Costantinopoli 16, 80138 Napoli, Italy;
| | - Ralf Moeller
- German Aerospace Center (DLR e.V.), Institute of Aerospace Medicine, Radiation Biology Department, Aerospace Microbiology, DLR, Linder Höhe, D-51147 Köln, Germany; or
- Natural Sciences Department, University of Applied Sciences Bonn-Rhein-Sieg (BRSU), von-Liebig-Straße 20, D-53359 Rheinbach, Germany
| | - Paola Di Donato
- Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei, 34, 80078 Pozzuoli, Italy; (I.R.); (A.P.)
- Department of Science and Technology, Parthenope University of Naples, Centro Direzionale—Isola C4, 80143 Napoli, Italy
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Transcript Regulation of the Recoded Archaeal α-l-Fucosidase In Vivo. Molecules 2021; 26:molecules26071861. [PMID: 33806142 PMCID: PMC8037382 DOI: 10.3390/molecules26071861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/22/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022] Open
Abstract
Genetic decoding is flexible, due to programmed deviation of the ribosomes from standard translational rules, globally termed "recoding". In Archaea, recoding has been unequivocally determined only for termination codon readthrough events that regulate the incorporation of the unusual amino acids selenocysteine and pyrrolysine, and for -1 programmed frameshifting that allow the expression of a fully functional α-l-fucosidase in the crenarchaeon Saccharolobus solfataricus, in which several functional interrupted genes have been identified. Increasing evidence suggests that the flexibility of the genetic code decoding could provide an evolutionary advantage in extreme conditions, therefore, the identification and study of interrupted genes in extremophilic Archaea could be important from an astrobiological point of view, providing new information on the origin and evolution of the genetic code and on the limits of life on Earth. In order to shed some light on the mechanism of programmed -1 frameshifting in Archaea, here we report, for the first time, on the analysis of the transcription of this recoded archaeal α-l-fucosidase and of its full-length mutant in different growth conditions in vivo. We found that only the wild type mRNA significantly increased in S. solfataricus after cold shock and in cells grown in minimal medium containing hydrolyzed xyloglucan as carbon source. Our results indicated that the increased level of fucA mRNA cannot be explained by transcript up-regulation alone. A different mechanism related to translation efficiency is discussed.
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Finore I, Vigneron A, Vincent WF, Leone L, Di Donato P, Schiano Moriello A, Nicolaus B, Poli A. Novel Psychrophiles and Exopolymers from Permafrost Thaw Lake Sediments. Microorganisms 2020; 8:microorganisms8091282. [PMID: 32842646 PMCID: PMC7563700 DOI: 10.3390/microorganisms8091282] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Thermokarst lakes are one of the most abundant types of microbial ecosystems in the circumpolar North. These shallow basins are formed by the thawing and collapse of ice-rich permafrost, with subsequent filling by snow and ice melt. Until now, permafrost thaw lakes have received little attention for isolation of microorganisms by culture-based analysis. The discovery of novel psychrophiles and their biomolecules makes these extreme environments suitable sources for the isolation of new strains, including for potential biotechnological applications. In this study, samples of bottom sediments were collected from three permafrost thaw lakes in subarctic Québec, Canada. Their diverse microbial communities were characterized by 16S rRNA gene amplicon analysis, and subsamples were cultured for the isolation of bacterial strains. Phenotypic and genetic characterization of the isolates revealed affinities to the genera Pseudomonas, Paenibacillus, Acinetobacter,Staphylococcus and Sphingomonas. The isolates were then evaluated for their production of extracellular enzymes and exopolymers. Enzymes of potential biotechnological interest included α and β-glucosidase, α and β-maltosidase, β-xylosidase and cellobiohydrolase. One isolate, Pseudomonas extremaustralis strain 2ASCA, also showed the capability to produce, in the loosely bound cell fraction, a levan-type polysaccharide with a yield of 613 mg/L of culture, suggesting its suitability as a candidate for eco-sustainable alternatives to commercial polymers.
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Affiliation(s)
- Ilaria Finore
- Consiglio Nazionale delle Ricerche C.N.R., Institute of Biomolecular Chemistry (ICB), via Campi Flegrei 34, 80078 Pozzuoli (Na), Italy; (I.F.); (L.L.); (P.D.D.); (A.S.M.); (B.N.)
| | - Adrien Vigneron
- Centre d’études nordiques (CEN) & Département de Biologie, Université Laval, Quebec City, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
| | - Warwick F. Vincent
- Centre d’études nordiques (CEN) & Département de Biologie, Université Laval, Quebec City, QC G1V 0A6, Canada; (A.V.); (W.F.V.)
| | - Luigi Leone
- Consiglio Nazionale delle Ricerche C.N.R., Institute of Biomolecular Chemistry (ICB), via Campi Flegrei 34, 80078 Pozzuoli (Na), Italy; (I.F.); (L.L.); (P.D.D.); (A.S.M.); (B.N.)
| | - Paola Di Donato
- Consiglio Nazionale delle Ricerche C.N.R., Institute of Biomolecular Chemistry (ICB), via Campi Flegrei 34, 80078 Pozzuoli (Na), Italy; (I.F.); (L.L.); (P.D.D.); (A.S.M.); (B.N.)
- Department of Science and Technology, University of Naples Parthenope, Centro Direzionale, Isola C4, 80143 Naples, Italy
| | - Aniello Schiano Moriello
- Consiglio Nazionale delle Ricerche C.N.R., Institute of Biomolecular Chemistry (ICB), via Campi Flegrei 34, 80078 Pozzuoli (Na), Italy; (I.F.); (L.L.); (P.D.D.); (A.S.M.); (B.N.)
| | - Barbara Nicolaus
- Consiglio Nazionale delle Ricerche C.N.R., Institute of Biomolecular Chemistry (ICB), via Campi Flegrei 34, 80078 Pozzuoli (Na), Italy; (I.F.); (L.L.); (P.D.D.); (A.S.M.); (B.N.)
| | - Annarita Poli
- Consiglio Nazionale delle Ricerche C.N.R., Institute of Biomolecular Chemistry (ICB), via Campi Flegrei 34, 80078 Pozzuoli (Na), Italy; (I.F.); (L.L.); (P.D.D.); (A.S.M.); (B.N.)
- Correspondence: ; Tel.: +39-0818675311
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Camerlingo C, Di Meo G, Lepore M, Lisitskiy M, Poli A, Portaccio M, Romano I, Di Donato P. Graphene-Based and Surface-Enhanced Raman Spectroscopy for Monitoring the Physio-Chemical Response of Thermophilic Bacterial Spores to Low Temperatures Exposure. SENSORS 2020; 20:s20154150. [PMID: 32722541 PMCID: PMC7435614 DOI: 10.3390/s20154150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/18/2020] [Accepted: 07/22/2020] [Indexed: 12/25/2022]
Abstract
Monitoring the spore life cycle is one of the main issues in several fields including environmental control, sustainable ecosystems, food security, and healthcare systems. In this framework, the study of the living organism resistance to extreme conditions like those mimicking space environments is particularly interesting. The assessment of the local change of the pH level can be extremely useful for this purpose. An optical physiometer method based on the Raman response of the graphene, which is able to locally sense pH of a fluid on a micrometric scale, has been recently proposed. Due to the presence of π-bonds at the surface, the electronic doping of graphene is determined by the external conditions and can be electrochemically controlled or altered by the contact with an acid or alkaline fluid. The doping level affects the vibrational energies of the graphene that can be monitored by conventional Raman spectroscopy. In addition, Surface-Enhanced Raman Spectroscopy (SERS) can give direct information on the biochemical changes occurring in spore components. In this work, we propose the joint use of Graphene-Based Raman Spectroscopy (GbRS) and SERS for the monitoring of the response of spores to exposure to low temperatures down to 100 K. The spores of the thermophilic bacterium Parageobacillus thermantarcticus isolated from an active volcano of Antarctica (Mt. Melbourne) were investigated. These spores are particularly resistant to several stressing stimuli and able to adapt to extreme conditions like low temperatures, UV irradiation, and γ-rays exposure. The results obtained showed that the joint use of GbRS and SERS represents a valuable tool for monitoring the physio-chemical response of bacterial spores upon exposure to stressing stimuli.
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Affiliation(s)
- Carlo Camerlingo
- CNR-SPIN, Institute for Superconductivity, Innovative Materials and Devices, 80078 Pozzuoli, Italy; (C.C.); (M.L.)
| | - Giuseppe Di Meo
- CNR-ICB, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy; (G.D.M.); (A.P.); (I.R.); (P.D.D.)
| | - Maria Lepore
- Dipartimento di Medicina Sperimentale, Università della Campania “L. Vanvitelli”, Via S. Maria di Costantinopoli 16, 80138 Napoli, Italy;
- Correspondence:
| | - Mikhail Lisitskiy
- CNR-SPIN, Institute for Superconductivity, Innovative Materials and Devices, 80078 Pozzuoli, Italy; (C.C.); (M.L.)
| | - Annarita Poli
- CNR-ICB, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy; (G.D.M.); (A.P.); (I.R.); (P.D.D.)
| | - Marianna Portaccio
- Dipartimento di Medicina Sperimentale, Università della Campania “L. Vanvitelli”, Via S. Maria di Costantinopoli 16, 80138 Napoli, Italy;
| | - Ida Romano
- CNR-ICB, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy; (G.D.M.); (A.P.); (I.R.); (P.D.D.)
| | - Paola Di Donato
- CNR-ICB, Institute of Biomolecular Chemistry, 80078 Pozzuoli, Italy; (G.D.M.); (A.P.); (I.R.); (P.D.D.)
- Dipartimento di Scienze e Tecnologie, Università Parthenope di Napoli, Centro Direzionale Isola C/4, 80143 Napoli, Italy
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Parageobacillus thermantarcticus, an Antarctic Cell Factory: From Crop Residue Valorization by Green Chemistry to Astrobiology Studies. DIVERSITY 2019. [DOI: 10.3390/d11080128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Knowledge of Antarctic habitat biodiversity, both marine and terrestrial, has increased considerably in recent years, causing considerable development in the studies of life science related to Antarctica. In the Austral summer 1986–1987, a new thermophilic bacterium, Parageobacillus thermantarcticus strain M1 was isolated from geothermal soil of the crater of Mount Melbourne (74°22′ S, 164°40′ E) during the Italian Antarctic Expedition. In addition to the biotechnological potential due to the production of exopolysaccharides and thermostable enzymes, successful studies have demonstrated its use in the green chemistry for the transformation and valorization of residual biomass and its employment as a suitable microbial model for astrobiology studies. The recent acquisition of its genome sequence opens up new opportunities for the use of this versatile bacterium in still unexplored biotechnology sectors.
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Peculiarities and biotechnological potential of environmental adaptation by Geobacillus species. Appl Microbiol Biotechnol 2018; 102:10425-10437. [PMID: 30310966 DOI: 10.1007/s00253-018-9422-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 12/21/2022]
Abstract
The genus Geobacillus comprises thermophilic bacilli capable of endospore formation. The members of this genus provide thermostable proteins and can be used in whole cell applications at elevated temperatures; therefore, these organisms are of biotechnological importance. While these applications have been described in previous reviews, the present paper highlights the environmental adaptations and genome diversifications of Geobacillus spp. and their applications in evolutionary-protein engineering. Despite their obligate thermophilic properties, Geobacillus spp. are widely distributed in nature. Because several isolates demonstrate remarkable properties for cell reproduction in their respective niches, they seem to exist not only as endospores but also as vegetative cells in diverse environments. This suggests their excellence in environmental adaptation via genome diversification; in fact, evidence suggests that Geobacillus spp. were derived from Bacillus spp. while diversifying their genomes via horizontal gene transfer. Moreover, when subjected to an environmental stressor, Geobacillus spp. diversify their genomes using inductive mutations and transposable elements to produce derivative cells that are adaptive to the stressor. Notably, inductive mutations in Geobacillus spp. occur more rapidly and frequently than the stress-induced mutagenesis observed in other microorganisms. Owing to this, Geobacillus spp. can efficiently generate mutant genes coding for thermostable enzyme variants from the thermolabile enzyme genes under appropriate selection pressures. This phenomenon provides a new approach to generate thermostable enzymes, termed as thermoadaptation-directed enzyme evolution, thereby expanding the biotechnological potentials of Geobacillus spp. In this review, we have discussed this approach using successful examples and major challenges yet to be addressed.
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Resistance and Raman spectroscopy analysis of Parageobacillus thermantarcticus spores after γ-ray exposure. Extremophiles 2018; 22:931-941. [PMID: 30120597 DOI: 10.1007/s00792-018-1049-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/08/2018] [Indexed: 01/17/2023]
Abstract
Spores of the genus Bacillus are able to resist ionizing radiations and therefore they are a suitable biological model for studies in Astrobiology, i.e. the multidisciplinary approach to the study of the origin and evolution of life on Earth and in the universe. The resistance to γ-radiation is an important issue in Astrobiology in relation to the search for bacterial species that could adapt to life in space. This study investigates the resistance of spores of the thermophilic bacteria Parageobacillus thermantarcticus to γ-rays. The analysis of spores' response to irradiation at a molecular level is performed by means of Raman spectroscopy that allows to get insights in the sequence of events taking place during inactivation. The role of the γ-rays' dose in the inactivation of spores is also investigated, allowing to highlight the mechanism(s) of inactivation including DNA damage, protein denaturation and calcium dipicolinate levels.
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